Figure-extended-data-Figure-6-code

Load packages and functions

library(EnhancedVolcano)
library(UCell)
library(ggpubr)
library(rstatix)
library(Seurat)
library(SingleCellExperiment)
library(harmony)
library(scDblFinder)
library(SeuratDisk)
library(SeuratWrappers)
library(assertthat)
library(tidyquant)
library(tidyverse)
library(viridis)
library(ComplexHeatmap)
library(Matrix)
library(tidyverse)
library(readxl)
library(broom)
library(ggbeeswarm)
library(RColorBrewer)
library(scCustomize)
library(SPATA2)
library(NICHES)
library(cowplot)
library(NICHES)
library(clusterProfiler)
library(biomaRt)

## load functions and colors
source("R/functions.R")

Extended Data Figure 6a - prepro

## add DAM signature
## DAM modules
## find human homologs
dams <- list("DAM"= data.frame("MGI.symbol"=c("Cts7","Lpl","Itgax","Spp1","Apoe","Csf1","Clec7a","Igf1","Axl","Ank","Cd63","Tyrobp","Ctsb","Ctsd","Ctsl","Cd9","Ctsz","Ccl6","Trem2")))
  dams <- bind_rows(dams, .id = "term")
  
  ## find homologs
  ensembl.human <-useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")   #useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
  ensembl.mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")  #useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl")
  
  homologs = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = dams$MGI.symbol , mart = ensembl.mouse, attributesL = c("hgnc_symbol"), martL = ensembl.human, uniqueRows=T)
  dams <- dams %>% 
    left_join(homologs)
  
  dam_markers <- list("DAM"=homologs$HGNC.symbol[-7])

## set the module scores
immune_comb <- AddModuleScore(immune_comb, dam_markers, name = names( dam_markers))

Error: object 'immune_comb' not found

Figure panels Extended data Figure 6 a,b,d

signatures <- c("macrophages_UCell","microglia_UCell","G2M.Score", "S.Score","DAM_UCell")

walk(signatures, function(x) {
  plt <- FeaturePlot(immune_comb, x) +
    scale_color_distiller(palette = "Reds", direction = 1) +
    theme_void()
  print(plt)
})

ED Figure 6 c

## subset the object for myeloid clusters
myeloid <- immune_comb[, !immune_comb$seurat_clusters %in% c("16","11","15","19","17")]

Figure panels Extended data Figure 6 e

immune_comb$dataset2 <- factor(immune_comb$dataset, levels = c("Braun et al.","Yang et al.","Present study"))

DimPlot(immune_comb, label = T, pt.size = .5, group.by = "dataset2") +
  scale_color_brewer(palette = "Paired") +
  labs(title = element_blank()) +
  theme_void()

Extended Data Figure 6f

Extended Data Figure 6g

Extended Data Figure 6h

DimPlot(fetal, group.by = "compartment", label = T, pt.size = 1, repel = T) +
  scale_color_manual(values = unname(palette_dark())[c(1:2,4)]) +
  theme_void() +
  NoLegend() +
  labs(title = element_blank())

fetal[[]] %>% 
  mosaicGG2(X="seurat_clusters",FILL="compartment", colors = unname(palette_dark())[c(1:2,4)])

Extended Data Figure 6i

DimPlot(fetal, group.by = "timepoint", label = T, pt.size = 1, repel = T) +
  scale_color_brewer(palette = "Set2") +
  theme_void() +
  NoLegend() +
  labs(title = element_blank())

## plot timepoint marimekko
fetal[[]] %>% 
  mosaicGG2(X="seurat_clusters",FILL="timepoint") +
  scale_fill_brewer(palette = "Set2")

Roman Sankowski 03-10-2023 email: roman.sankowski@uniklinik-freiburg.de